Re: [gmx-users] GMX-PLUMED speed

They have a forum! I do agree it is more appropriate there! Tks, X- > On 05 Feb 2017, at 17:19, Justin Lemkul wrote: > > > > On 2/5/17 3:49 AM, XAvier Periole wrote: >> >> Dears, >> >> I am using gromacs v5.1.4 with PLUMED v2.3.0. >> >>

[gmx-users] GMX-PLUMED speed

Dears, I am using gromacs v5.1.4 with PLUMED v2.3.0. Through my experience as a novice in using PLUMED, I have noticed that not writing the restraint/forces info in a file and not using a STRIDE accelerate the code significantly. Using a line such as follows in the plumed parameters set: PRI

Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

able if anyone ever wants to do it in the future. >> ____________ >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of XAvier >> Periole >> Sent: 01 February 2017 11:18:36 >> To: gmx-us...@gromacs.org >

Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

What about tilling 2x2 and then removing lipids that have x&y larger than a cutoff … then minimisation+equilibration of the interface even atomistic would be quite trivial. X- > On 01 Feb 2017, at 17:14, Christopher Neale > wrote: > > Dear Users: > > I have some atomistic systems of a memb

Re: [gmx-users] Inverse CG MARTINI trajectory

There is an older tool than backward accessible on cgmartini.nl , it is in the reverse section … works with an older version of gmx. I believe other people have developed similar tools but not sure that they work on xtc. But I’d be suggesting you try to contact Tsjerk on

[gmx-users] trouble using tables with 5.1

Dears, Note: At the end of the message I provide a solution found while writing the email ... I am having troubles feeding mdrun my tabulated bonded terms through tables. The manual does not indicate any change in that respect … I used to run this with gmx-463 with the command looking like: m

Re: [gmx-users] Using ATB to generate valid topologies

-014-9713-7> X- > On 13 Jul 2016, at 17:39, Justin Lemkul wrote: > > > > On 7/13/16 11:02 AM, XAvier Periole wrote: >>>> >>>> Just for the record ATB is a very good tool to build a start up topology. >>>> They also have a large set of topologi

Re: [gmx-users] Using ATB to generate valid topologies

>> >> Just for the record ATB is a very good tool to build a start up topology. >> They also have a large set of topologies available on the site. >> >> The charges are determined by QM and the user chooses the level of accuracy. >> The bonded and LJ parameters are chosen based on the type of at

Re: [gmx-users] Using ATB to generate valid topologies

Just for the record ATB is a very good tool to build a start up topology. They also have a large set of topologies available on the site. The charges are determined by QM and the user chooses the level of accuracy. The bonded and LJ parameters are chosen based on the type of atom and it conne

Re: [gmx-users] [pairs] vs [exclusions]

Hi Peter, Wouldn’t the exclusion act on the regular LJ and pairs add a different LJ(14)? With exclusions, do you have the regular LJ present? XAvier. > On 13 Jul 2016, at 13:17, Peter Kroon wrote: > > Hi Mark (and list), > > thanks for the ideas. > `gmx check -s1 with_excl.tpr -s2 no_excl.

Re: [gmx-users] elastic restraints in MARTINI simulation

Any reference to illustrate the unphysical behavior of macromolecular systems using Berendsen thermostat compare to others? XAvier. > On Mar 23, 2016, at 10:42, James Starlight wrote: > > Btw taking back to my question regarding thermostats in CG sims- does > the correct choise influence on

Re: [gmx-users] Gromacs Tutorial

Bastards … On Jan 19, 2016, at 2:00 PM, Tsjerk Wassenaar wrote: > Hey :) > > As some of you know, some years ago I developed an extensive Gromacs > tutorial (at the University of Utrecht). That work has caught they eye of > educators, and now the tutorial is published as an educational paper!

Re: [gmx-users] regarding glycolipids parameters for GROMACS

Hi, A set of exotic lipids compatible with GROMOS should be available soon too :)). XAvier. > On Mar 3, 2015, at 23:06, Carlos Navarro Retamal wrote: > > Dear gromacs users, > I was wondering, are they glycolipids (MGDG more specifically) parameters > availably for gromacs package? it do

Re: [gmx-users] clustering using gromos method

onal de San Luis >> IMASL-CONICET >> San Luis, Argentina >> >> Tel..:+54 266 4424689 int 6153 >> e-mail...: adga...@unsl.edu.ar >> e-mail...: adrianagarr...@gmail.com >> >> >> ** >> >> 2015-01-12 17:12 GMT+01:00 XAvier Periole : >

Re: [gmx-users] clustering using gromos method

with the gromos method the criteria is the RMSD between the structure of the objects given to cluster …. two neighbours are two structures that are within this cutoff (eg. 0.25) obviously defining an RMSD between the two objects should make sense. On Jan 12, 2015, at 4:56 PM, Adriana Garro w

Re: [gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

The warning of grompp says you have two charge groups (bound groups from a molecule) at 7 nm, while the cutoff of theses interactions is 1 nm! This most likely reflects a broken molecule … Visualising your system indicates it is broken all over the place at the PBC. Make your molecule whole f

Re: [gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

Could be a water molecule broken at the box limits. Try to rebuild the water molecules before minimizing. Trjconv -pbc mol -f in.gro -o out.gro would do it. > On Jan 11, 2015, at 00:17, Jonathan Saboury wrote: > > My system is blowing up during minimization. I'm getting the error: > ---

Re: [gmx-users] martinize.py: option for partly have elastic network on partly in the protein

There is no specific option to do this but you can go in the itp file where the electric network is defined and comment out the section corresponding to the n-terminus. > On Dec 18, 2014, at 14:57, shivangi nangia wrote: > > Dear gmx-users, > > I wish to coarse grain a peptide, while keepi

Re: [gmx-users] Martini force field for inhibitors

There are a few review article where the strategy and guidelines are described. You can find this material on the cgmartini.nl website. > On Aug 29, 2014, at 2:03, Sridhar Kumar Kannam wrote: > > Dear Gromacs users, > > I have very recently started working with Gromacs and Martini force fie

Re: [gmx-users] Archaeal lipid packages for Gromos 53A6

If you want to stick to the GROMOS force field family you'd want to use the gromos-54A7/8 J. Chem. Theory Comput., 2013, 9 (2), pp 1247–1264, DOI: 10.1021/ct300874c CHARMM over-stabilizes helices. On Aug 12, 2014, at 5:12 PM, Justin Lemkul wrote: > > > On 8/12/14, 11:08 AM, Wainwright, Jo

Re: [gmx-users] Use g_wham on 2D PMF

g_wham does only 1D PMF but can handle several restrains. There is 2D code on Alan Grossfield website. Plumed refers to it. On Feb 3, 2014, at 5:54 PM, "DAI, JIAN" wrote: > Dear all: > Is it possible for g_wham to calculate 2D PMF? > It seems to me that g_wham can deal with this because the

Re: [gmx-users] Bond interaction exclusions

Hi, The first line "eth1" tells it all. In that molecule all non-bonded interactions between first bonded neighbors will be excluded. Thus the 1-3, 1-4 (and so on) non-bonded interactions will be included. You may add additional exclusions in the [ exclusion ] section of your topology.

Re: [gmx-users] charge correction in topology file from PRODRG

For gromos ff you can also use the ATB server. From Alan Mark on Brisbane. It combine typography and non-bonded parameters all at once. It is not perfect but pretty good. > On Dec 8, 2013, at 8:27, Mahboobeh Eslami wrote: > > hi all my friends > I use PRODRG and antechmber for building topo

Re: [gmx-users] end capping

You can choose different termini by setting the option term (-term) to pdb2gmx. The ff gromos 53a6 has a strong tendency to destabilize alpha helices and favors sheets. If you like to stick to gromos ff you need to switch to the 54a7 more recent version to which a rectification of this bias ha

Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

gt; my mpirun and/or OpenMP library was setting thread affinities for me. That > may or may not have been the case for you. Can you please open an issue at > redmine.gromacs.org with .tpr, .log, stdout, stderr for both a working and > failing case? > > Mark > > > On Mon

Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

For the record. gmx-4.6.4 hangs when number of threads is not a multiple of the number of nodes. XAvier. On Nov 22, 2013, at 7:14 PM, XAvier Periole wrote: > > Ok, tks. I'll try then :)) > > XAvier. > > On Nov 22, 2013, at 4:31 PM, Mark Abraham wrote: >

Re: [gmx-users] Martini and Gromacs 3 and 4

Yes you can use MARTINI with any GMX. On Nov 22, 2013, at 8:16 PM, Steve Seibold wrote: > Hello > I was under the impression that I needed Gromacs 3.3.1 to implement the > Martini FF. But as I have been looking at mdp files for Martini, I am finding > statements about this mdp file to be use

Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

> On Nov 21, 2013 7:37 PM, "XAvier Periole" wrote: > >> >> For the record: >> >> I do not expect this issue to be affected by an update to gmx4.6.4 … >> >> But the problem is fixed by turning the pin option off. >> >> XAvier. &g

Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

sues > is with 4.6.1, you should really update to the latest version. If the > problem persists with 4.6.4, we shall have a closer look. > > Cheers, > -- > Szilárd > > > On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole wrote: >> >> Dears, >> >

[gmx-users] # of threads different than # of cores -> gmx hangs.

Dears, When running on multiple nodes I get GMX-461 hanging if the number of threads is not a multiple of the number of cores. example: with 11 nodes having 24 cores each, defining 253 threads (23 threads per node) or 264 threads (24 threads per node) would work but defining 256 threads would

Re: [gmx-users] MD simulations in the presence of osmolytes

That would be a question for the developers of the force fields. You can start by a google search of the osmolytes and force filed keywords ... > On Nov 19, 2013, at 2:23, Amjad Farooq wrote: > > Hi everyone, > > I am wondering whether it is possible to conduct MD simulations on a > protein